-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package MCview;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-\r
-import jalview.appletgui.*;\r
-import jalview.structure.*;\r
-\r
-public class AppletPDBCanvas\r
- extends Panel implements MouseListener, MouseMotionListener, StructureListener\r
-{\r
-\r
- MCMatrix idmat = new MCMatrix(3, 3);\r
- MCMatrix objmat = new MCMatrix(3, 3);\r
- boolean redrawneeded = true;\r
- int omx = 0;\r
- int mx = 0;\r
- int omy = 0;\r
- int my = 0;\r
- public PDBfile pdb;\r
- PDBEntry pdbentry;\r
- int bsize;\r
- Image img;\r
- Graphics ig;\r
- Dimension prefsize;\r
- float[] centre = new float[3];\r
- float[] width = new float[3];\r
- float maxwidth;\r
- float scale;\r
- String inStr;\r
- String inType;\r
- boolean bysequence = true;\r
- boolean depthcue = true;\r
- boolean wire = false;\r
- boolean bymolecule = false;\r
- boolean zbuffer = true;\r
- boolean dragging;\r
- int xstart;\r
- int xend;\r
- int ystart;\r
- int yend;\r
- int xmid;\r
- int ymid;\r
- Font font = new Font("Helvetica", Font.PLAIN, 10);\r
- public SequenceI [] sequence;\r
- final StringBuffer mappingDetails = new StringBuffer();\r
- String appletToolTip = null;\r
- int toolx, tooly;\r
- PDBChain mainchain;\r
- Vector highlightRes;\r
- boolean pdbAction = false;\r
- Bond highlightBond1, highlightBond2;\r
- boolean errorLoading = false;\r
- boolean seqColoursReady = false;\r
- FeatureRenderer fr;\r
- AlignmentPanel ap;\r
- StructureSelectionManager ssm;\r
-\r
- public AppletPDBCanvas(PDBEntry pdbentry,\r
- SequenceI[] seq,\r
- AlignmentPanel ap,\r
- String protocol)\r
-\r
- {\r
- this.ap = ap;\r
- this.pdbentry = pdbentry;\r
- this.sequence = seq;\r
-\r
- ssm = StructureSelectionManager.getStructureSelectionManager();\r
-\r
- try{\r
- pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);\r
- }catch(Exception ex)\r
- {\r
- ex.printStackTrace();\r
- return;\r
- }\r
-\r
- pdbentry.setId(pdb.id);\r
-\r
- ssm.addStructureViewerListener(this);\r
-\r
- colourBySequence(ap.getSequenceRenderer(),\r
- ap.av.getShowSequenceFeatures() ?\r
- ap.getFeatureRenderer() : null);\r
-\r
- int max = -10;\r
- int maxchain = -1;\r
- int pdbstart = 0;\r
- int pdbend = 0;\r
- int seqstart = 0;\r
- int seqend = 0;\r
- AlignSeq maxAlignseq = null;\r
-\r
- //JUST DEAL WITH ONE SEQUENCE FOR NOW\r
- SequenceI sequence = seq[0];\r
-\r
- for (int i = 0; i < pdb.chains.size(); i++)\r
- {\r
-\r
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +\r
- ( (PDBChain) pdb.chains.elementAt(i)).sequence.\r
- getSequenceAsString());\r
- mappingDetails.append("\nNo of residues = " +\r
- ( (PDBChain) pdb.chains.elementAt(i)).residues.size() +\r
- "\n\n");\r
-\r
- // Now lets compare the sequences to get\r
- // the start and end points.\r
- // Align the sequence to the pdb\r
- AlignSeq as = new AlignSeq(sequence,\r
- ( (PDBChain) pdb.chains.elementAt(i)).sequence,\r
- "pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- PrintStream ps = new PrintStream(System.out)\r
- {\r
- public void print(String x)\r
- {\r
- mappingDetails.append(x);\r
- }\r
-\r
- public void println()\r
- {\r
- mappingDetails.append("\n");\r
- }\r
- };\r
-\r
- as.printAlignment(ps);\r
-\r
- if (as.maxscore > max)\r
- {\r
- max = as.maxscore;\r
- maxchain = i;\r
-\r
- pdbstart = as.seq2start;\r
- pdbend = as.seq2end;\r
- seqstart = as.seq1start + sequence.getStart() - 1;\r
- seqend = as.seq1end + sequence.getEnd() - 1;\r
- maxAlignseq = as;\r
- }\r
-\r
- mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);\r
- mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);\r
- }\r
-\r
- mainchain = (PDBChain) pdb.chains.elementAt(maxchain);\r
-\r
- mainchain.pdbstart = pdbstart;\r
- mainchain.pdbend = pdbend;\r
- mainchain.seqstart = seqstart;\r
- mainchain.seqend = seqend;\r
- mainchain.isVisible = true;\r
- // mainchain.makeExactMapping(maxAlignseq, sequence);\r
- // mainchain.transferRESNUMFeatures(sequence, null);\r
- this.pdb = pdb;\r
- this.prefsize = new Dimension(getSize().width, getSize().height);\r
-\r
- //Initialize the matrices to identity\r
- for (int i = 0; i < 3; i++)\r
- {\r
- for (int j = 0; j < 3; j++)\r
- {\r
- if (i != j)\r
- {\r
- idmat.addElement(i, j, 0);\r
- objmat.addElement(i, j, 0);\r
- }\r
- else\r
- {\r
- idmat.addElement(i, j, 1);\r
- objmat.addElement(i, j, 1);\r
- }\r
- }\r
- }\r
-\r
- addMouseMotionListener(this);\r
- addMouseListener(this);\r
-\r
- addKeyListener(new KeyAdapter()\r
- {\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- doKeyPressed(evt);\r
- }\r
- });\r
-\r
- findCentre();\r
- findWidth();\r
-\r
- setupBonds();\r
-\r
- scale = findScale();\r
- }\r
-\r
- Vector visiblebonds;\r
- void setupBonds()\r
- {\r
- seqColoursReady = false;\r
- // Sort the bonds by z coord\r
- visiblebonds = new Vector();\r
-\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)\r
- {\r
- Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
-\r
- for (int i = 0; i < tmp.size(); i++)\r
- {\r
- visiblebonds.addElement(tmp.elementAt(i));\r
- }\r
- }\r
- }\r
- seqColoursReady = true;\r
- colourBySequence(ap.getSequenceRenderer(),\r
- ap.av.getShowSequenceFeatures() ?\r
- ap.getFeatureRenderer() : null);\r
- redrawneeded = true;\r
- repaint();\r
- }\r
-\r
- public void findWidth()\r
- {\r
- float[] max = new float[3];\r
- float[] min = new float[3];\r
-\r
- max[0] = (float) - 1e30;\r
- max[1] = (float) - 1e30;\r
- max[2] = (float) - 1e30;\r
-\r
- min[0] = (float) 1e30;\r
- min[1] = (float) 1e30;\r
- min[2] = (float) 1e30;\r
-\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)\r
- {\r
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
-\r
- for (int i = 0; i < bonds.size(); i++)\r
- {\r
- Bond tmp = (Bond) bonds.elementAt(i);\r
-\r
- if (tmp.start[0] >= max[0])\r
- {\r
- max[0] = tmp.start[0];\r
- }\r
-\r
- if (tmp.start[1] >= max[1])\r
- {\r
- max[1] = tmp.start[1];\r
- }\r
-\r
- if (tmp.start[2] >= max[2])\r
- {\r
- max[2] = tmp.start[2];\r
- }\r
-\r
- if (tmp.start[0] <= min[0])\r
- {\r
- min[0] = tmp.start[0];\r
- }\r
-\r
- if (tmp.start[1] <= min[1])\r
- {\r
- min[1] = tmp.start[1];\r
- }\r
-\r
- if (tmp.start[2] <= min[2])\r
- {\r
- min[2] = tmp.start[2];\r
- }\r
-\r
- if (tmp.end[0] >= max[0])\r
- {\r
- max[0] = tmp.end[0];\r
- }\r
-\r
- if (tmp.end[1] >= max[1])\r
- {\r
- max[1] = tmp.end[1];\r
- }\r
-\r
- if (tmp.end[2] >= max[2])\r
- {\r
- max[2] = tmp.end[2];\r
- }\r
-\r
- if (tmp.end[0] <= min[0])\r
- {\r
- min[0] = tmp.end[0];\r
- }\r
-\r
- if (tmp.end[1] <= min[1])\r
- {\r
- min[1] = tmp.end[1];\r
- }\r
-\r
- if (tmp.end[2] <= min[2])\r
- {\r
- min[2] = tmp.end[2];\r
- }\r
- }\r
- }\r
- }\r
-\r
- width[0] = (float) Math.abs(max[0] - min[0]);\r
- width[1] = (float) Math.abs(max[1] - min[1]);\r
- width[2] = (float) Math.abs(max[2] - min[2]);\r
-\r
- maxwidth = width[0];\r
-\r
- if (width[1] > width[0])\r
- {\r
- maxwidth = width[1];\r
- }\r
-\r
- if (width[2] > width[1])\r
- {\r
- maxwidth = width[2];\r
- }\r
-\r
- // System.out.println("Maxwidth = " + maxwidth);\r
- }\r
-\r
- public float findScale()\r
- {\r
- int dim;\r
- int width;\r
- int height;\r
-\r
- if (getSize().width != 0)\r
- {\r
- width = getSize().width;\r
- height = getSize().height;\r
- }\r
- else\r
- {\r
- width = prefsize.width;\r
- height = prefsize.height;\r
- }\r
-\r
- if (width < height)\r
- {\r
- dim = width;\r
- }\r
- else\r
- {\r
- dim = height;\r
- }\r
-\r
- return (float) (dim / (1.5d * maxwidth));\r
- }\r
-\r
- public void findCentre()\r
- {\r
- float xtot = 0;\r
- float ytot = 0;\r
- float ztot = 0;\r
-\r
- int bsize = 0;\r
-\r
- //Find centre coordinate\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
- if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)\r
- {\r
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
-\r
- bsize += bonds.size();\r
-\r
- for (int i = 0; i < bonds.size(); i++)\r
- {\r
- xtot = xtot + ( (Bond) bonds.elementAt(i)).start[0] +\r
- ( (Bond) bonds.elementAt(i)).end[0];\r
-\r
- ytot = ytot + ( (Bond) bonds.elementAt(i)).start[1] +\r
- ( (Bond) bonds.elementAt(i)).end[1];\r
-\r
- ztot = ztot + ( (Bond) bonds.elementAt(i)).start[2] +\r
- ( (Bond) bonds.elementAt(i)).end[2];\r
- }\r
- }\r
- }\r
-\r
- centre[0] = xtot / (2 * (float) bsize);\r
- centre[1] = ytot / (2 * (float) bsize);\r
- centre[2] = ztot / (2 * (float) bsize);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
-\r
- if (errorLoading)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setColor(Color.black);\r
- g.setFont(new Font("Verdana", Font.BOLD, 14));\r
- g.drawString("Error loading PDB data!!", 50, getSize().height / 2);\r
- return;\r
- }\r
-\r
- if (!seqColoursReady)\r
- {\r
- g.setColor(Color.black);\r
- g.setFont(new Font("Verdana", Font.BOLD, 14));\r
- g.drawString("Fetching PDB data...", 50, getSize().height / 2);\r
- return;\r
- }\r
-\r
- //Only create the image at the beginning -\r
- //this saves much memory usage\r
- if ( (img == null) || (prefsize.width != getSize().width) ||\r
- (prefsize.height != getSize().height))\r
- {\r
-\r
- try\r
- {\r
- prefsize.width = getSize().width;\r
- prefsize.height = getSize().height;\r
-\r
- scale = findScale();\r
- img = createImage(prefsize.width, prefsize.height);\r
- ig = img.getGraphics();\r
-\r
- redrawneeded = true;\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- if (redrawneeded)\r
- {\r
- drawAll(ig, prefsize.width, prefsize.height);\r
- redrawneeded = false;\r
- }\r
- if (appletToolTip != null)\r
- {\r
- ig.setColor(Color.red);\r
- ig.drawString(appletToolTip, toolx, tooly);\r
- }\r
-\r
- g.drawImage(img, 0, 0, this);\r
-\r
- pdbAction = false;\r
- }\r
-\r
- public void drawAll(Graphics g, int width, int height)\r
- {\r
- ig.setColor(Color.black);\r
- ig.fillRect(0, 0, width, height);\r
- drawScene(ig);\r
- drawLabels(ig);\r
- }\r
-\r
- public void setColours(jalview.schemes.ColourSchemeI cs)\r
- {\r
- bysequence = false;\r
- pdb.setColours(cs);\r
- redrawneeded = true;\r
- repaint();\r
- }\r
-\r
-\r
-\r
- // This method has been taken out of PDBChain to allow\r
- // Applet and Application specific sequence renderers to be used\r
- void colourBySequence(SequenceRenderer sr, FeatureRenderer fr)\r
- {\r
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());\r
-\r
- boolean showFeatures = false;\r
- if (fr!=null)\r
- {\r
- if (fr == null)\r
- {\r
- fr = new jalview.appletgui.FeatureRenderer(ap.av);\r
- }\r
- fr.transferSettings(fr);\r
- showFeatures = true;\r
- }\r
-\r
- PDBChain chain;\r
- if (bysequence && pdb != null)\r
- {\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
- chain = (PDBChain) pdb.chains.elementAt(ii);\r
-\r
- for (int i = 0; i < chain.bonds.size(); i++)\r
- {\r
- Bond tmp = (Bond) chain.bonds.elementAt(i);\r
- tmp.startCol = Color.lightGray;\r
- tmp.endCol = Color.lightGray;\r
- if (chain != mainchain)\r
- {\r
- continue;\r
- }\r
-\r
- for (int s = 0; s < sequence.length; s++)\r
- {\r
- for (int m = 0; m < mapping.length; m++)\r
- {\r
- if (mapping[m].getSequence() == sequence[s])\r
- {\r
- int pos = mapping[m].getSeqPos(tmp.at1.resNumber)-1;\r
- if (pos > 0)\r
- {\r
- pos = sequence[s].findIndex(pos);\r
- tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);\r
- if (showFeatures)\r
- {\r
- tmp.startCol = fr.findFeatureColour(tmp.startCol,\r
- sequence[s],\r
- pos);\r
- }\r
- }\r
- pos = mapping[m].getSeqPos(tmp.at2.resNumber)-1;\r
- if (pos > 0)\r
- {\r
- pos = sequence[s].findIndex(pos);\r
- tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);\r
- if (showFeatures)\r
- {\r
- tmp.endCol = fr.findFeatureColour(tmp.endCol,\r
- sequence[s],\r
- pos);\r
- }\r
- }\r
-\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- Zsort zsort;\r
- public void drawScene(Graphics g)\r
- {\r
- if (zbuffer)\r
- {\r
- if (zsort == null)\r
- {\r
- zsort = new Zsort();\r
- }\r
-\r
- zsort.Zsort(visiblebonds);\r
- }\r
-\r
- Bond tmpBond = null;\r
- for (int i = 0; i < visiblebonds.size(); i++)\r
- {\r
- tmpBond = (Bond) visiblebonds.elementAt(i);\r
-\r
- xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +\r
- (getSize().width / 2));\r
- ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +\r
- (getSize().height / 2));\r
-\r
- xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +\r
- (getSize().width / 2));\r
- yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +\r
- (getSize().height / 2));\r
-\r
- xmid = (xend + xstart) / 2;\r
- ymid = (yend + ystart) / 2;\r
-\r
- if (depthcue && !bymolecule)\r
- {\r
- if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))\r
- {\r
- g.setColor(tmpBond.startCol.darker().darker());\r
- drawLine(g, xstart, ystart, xmid, ymid);\r
-\r
- g.setColor(tmpBond.endCol.darker().darker());\r
- drawLine(g, xmid, ymid, xend, yend);\r
- }\r
- else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))\r
- {\r
- g.setColor(tmpBond.startCol.darker());\r
- drawLine(g, xstart, ystart, xmid, ymid);\r
-\r
- g.setColor(tmpBond.endCol.darker());\r
- drawLine(g, xmid, ymid, xend, yend);\r
- }\r
- else\r
- {\r
- g.setColor(tmpBond.startCol);\r
- drawLine(g, xstart, ystart, xmid, ymid);\r
-\r
- g.setColor(tmpBond.endCol);\r
- drawLine(g, xmid, ymid, xend, yend);\r
- }\r
-\r
- }\r
- else if (depthcue && bymolecule)\r
- {\r
- if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))\r
- {\r
- g.setColor(Color.green.darker().darker());\r
- drawLine(g, xstart, ystart, xend, yend);\r
- }\r
- else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))\r
- {\r
- g.setColor(Color.green.darker());\r
- drawLine(g, xstart, ystart, xend, yend);\r
- }\r
- else\r
- {\r
- g.setColor(Color.green);\r
- drawLine(g, xstart, ystart, xend, yend);\r
- }\r
- }\r
- else if (!depthcue && !bymolecule)\r
- {\r
- g.setColor(tmpBond.startCol);\r
- drawLine(g, xstart, ystart, xmid, ymid);\r
- g.setColor(tmpBond.endCol);\r
- drawLine(g, xmid, ymid, xend, yend);\r
- }\r
- else\r
- {\r
- drawLine(g, xstart, ystart, xend, yend);\r
- }\r
-\r
- if (highlightBond1 != null && highlightBond1 == tmpBond)\r
- {\r
- g.setColor(Color.white);\r
- drawLine(g, xmid, ymid, xend, yend);\r
- }\r
-\r
- if (highlightBond2 != null && highlightBond2 == tmpBond)\r
- {\r
- g.setColor(Color.white);\r
- drawLine(g, xstart, ystart, xmid, ymid);\r
- }\r
-\r
- }\r
- }\r
-\r
- public void drawLine(Graphics g, int x1, int y1, int x2, int y2)\r
- {\r
- if (!wire)\r
- {\r
- if ( ( (float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)\r
- {\r
- g.drawLine(x1, y1, x2, y2);\r
- g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);\r
- g.drawLine(x1, y1 - 1, x2, y2 - 1);\r
- }\r
- else\r
- {\r
- g.setColor(g.getColor().brighter());\r
- g.drawLine(x1, y1, x2, y2);\r
- g.drawLine(x1 + 1, y1, x2 + 1, y2);\r
- g.drawLine(x1 - 1, y1, x2 - 1, y2);\r
- }\r
- }\r
- else\r
- {\r
- g.drawLine(x1, y1, x2, y2);\r
- }\r
- }\r
-\r
- public Dimension minimumsize()\r
- {\r
- return prefsize;\r
- }\r
-\r
- public Dimension preferredsize()\r
- {\r
- return prefsize;\r
- }\r
-\r
- public void doKeyPressed(KeyEvent evt)\r
- {\r
- if (evt.getKeyCode() == KeyEvent.VK_UP)\r
- {\r
- scale = (float) (scale * 1.1);\r
- redrawneeded = true;\r
- repaint();\r
- }\r
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)\r
- {\r
- scale = (float) (scale * 0.9);\r
- redrawneeded = true;\r
- repaint();\r
- }\r
- }\r
-\r
- public void mousePressed(MouseEvent e)\r
- {\r
- pdbAction = true;\r
- Atom fatom = findAtom(e.getX(), e.getY());\r
- if (fatom != null)\r
- {\r
- fatom.isSelected = !fatom.isSelected;\r
-\r
- redrawneeded = true;\r
- repaint();\r
- if (foundchain != -1)\r
- {\r
- PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
- if (chain == mainchain)\r
- {\r
- if (fatom.alignmentMapping != -1)\r
- {\r
- if (highlightRes == null)\r
- {\r
- highlightRes = new Vector();\r
- }\r
-\r
- if (highlightRes.contains(fatom.alignmentMapping + "" + ""))\r
- {\r
- highlightRes.removeElement(fatom.alignmentMapping + "");\r
- }\r
- else\r
- {\r
- highlightRes.addElement(fatom.alignmentMapping + "");\r
- }\r
- }\r
- }\r
- }\r
-\r
- }\r
- mx = e.getX();\r
- my = e.getY();\r
- omx = mx;\r
- omy = my;\r
- dragging = false;\r
- }\r
-\r
- public void mouseMoved(MouseEvent e)\r
- {\r
- pdbAction = true;\r
- if (highlightBond1 != null)\r
- {\r
- highlightBond1.at2.isSelected = false;\r
- highlightBond2.at1.isSelected = false;\r
- highlightBond1 = null;\r
- highlightBond2 = null;\r
- }\r
-\r
- Atom fatom = findAtom(e.getX(), e.getY());\r
-\r
- PDBChain chain = null;\r
- if (foundchain != -1)\r
- {\r
- chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
- if (chain == mainchain)\r
- {\r
- mouseOverStructure(fatom.resNumber, chain.id);\r
- }\r
- }\r
-\r
- if (fatom != null)\r
- {\r
- toolx = e.getX();\r
- tooly = e.getY();\r
-\r
- appletToolTip = chain.id + ":" + fatom.resNumber + " " + fatom.resName;\r
- redrawneeded = true;\r
- repaint();\r
- }\r
- else\r
- {\r
- mouseOverStructure(-1, chain!=null?chain.id:null);\r
- appletToolTip = null;\r
- redrawneeded = true;\r
- repaint();\r
- }\r
- }\r
-\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- }\r
-\r
- public void mouseEntered(MouseEvent e)\r
- {\r
- }\r
-\r
- public void mouseExited(MouseEvent e)\r
- {\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- int x = evt.getX();\r
- int y = evt.getY();\r
- mx = x;\r
- my = y;\r
-\r
- MCMatrix objmat = new MCMatrix(3, 3);\r
- objmat.setIdentity();\r
-\r
- if ( (evt.getModifiers() & Event.META_MASK) != 0)\r
- {\r
- objmat.rotatez( (float) ( (mx - omx)));\r
- }\r
- else\r
- {\r
- objmat.rotatex( (float) ( (my - omy)));\r
- objmat.rotatey( (float) ( (omx - mx)));\r
- }\r
-\r
- //Alter the bonds\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
-\r
- for (int i = 0; i < bonds.size(); i++)\r
- {\r
- Bond tmpBond = (Bond) bonds.elementAt(i);\r
-\r
- //Translate the bond so the centre is 0,0,0\r
- tmpBond.translate( -centre[0], -centre[1], -centre[2]);\r
-\r
- //Now apply the rotation matrix\r
- tmpBond.start = objmat.vectorMultiply(tmpBond.start);\r
- tmpBond.end = objmat.vectorMultiply(tmpBond.end);\r
-\r
- //Now translate back again\r
- tmpBond.translate(centre[0], centre[1], centre[2]);\r
- }\r
- }\r
-\r
- objmat = null;\r
-\r
- omx = mx;\r
- omy = my;\r
-\r
- dragging = true;\r
-\r
- redrawneeded = true;\r
-\r
- repaint();\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- dragging = false;\r
- return;\r
- }\r
-\r
- void drawLabels(Graphics g)\r
- {\r
-\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
-\r
- if (chain.isVisible)\r
- {\r
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
-\r
- for (int i = 0; i < bonds.size(); i++)\r
- {\r
- Bond tmpBond = (Bond) bonds.elementAt(i);\r
-\r
- if (tmpBond.at1.isSelected)\r
- {\r
- labelAtom(g, tmpBond, 1);\r
- }\r
-\r
- if (tmpBond.at2.isSelected)\r
- {\r
-\r
- labelAtom(g, tmpBond, 2);\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void labelAtom(Graphics g, Bond b, int n)\r
- {\r
- g.setFont(font);\r
-\r
- if (n == 1)\r
- {\r
- int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +\r
- (getSize().width / 2));\r
- int ystart = (int) ( ( (b.start[1] - centre[1]) * scale) +\r
- (getSize().height / 2));\r
-\r
- g.setColor(Color.red);\r
- g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);\r
- }\r
-\r
- if (n == 2)\r
- {\r
- int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +\r
- (getSize().width / 2));\r
- int ystart = (int) ( ( (b.end[1] - centre[1]) * scale) +\r
- (getSize().height / 2));\r
-\r
- g.setColor(Color.red);\r
- g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);\r
- }\r
- }\r
-\r
- int foundchain = -1;\r
- public Atom findAtom(int x, int y)\r
- {\r
- Atom fatom = null;\r
-\r
- foundchain = -1;\r
-\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
- int truex;\r
- Bond tmpBond = null;\r
-\r
- if (chain.isVisible)\r
- {\r
- Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;\r
-\r
- for (int i = 0; i < bonds.size(); i++)\r
- {\r
- tmpBond = (Bond) bonds.elementAt(i);\r
-\r
- truex = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +\r
- (getSize().width / 2));\r
-\r
- if (Math.abs(truex - x) <= 2)\r
- {\r
- int truey = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +\r
- (getSize().height / 2));\r
-\r
- if (Math.abs(truey - y) <= 2)\r
- {\r
- fatom = tmpBond.at1;\r
- foundchain = ii;\r
- break;\r
- }\r
- }\r
- }\r
-\r
- // Still here? Maybe its the last bond\r
-\r
- truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +\r
- (getSize().width / 2));\r
-\r
- if (Math.abs(truex - x) <= 2)\r
- {\r
- int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +\r
- (getSize().height / 2));\r
-\r
- if (Math.abs(truey - y) <= 2)\r
- {\r
- fatom = tmpBond.at2;\r
- foundchain = ii;\r
- break;\r
- }\r
- }\r
-\r
- }\r
-\r
- if (fatom != null) //)&& chain.ds != null)\r
- {\r
- chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
- }\r
- }\r
-\r
- return fatom;\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void highlightRes(int ii)\r
- {\r
- if (!seqColoursReady)\r
- {\r
- return;\r
- }\r
-\r
- if (highlightRes != null\r
- && highlightRes.contains( (ii - 1) + ""))\r
- {\r
- return;\r
- }\r
-\r
- int index = -1;\r
- Bond tmpBond;\r
- for (index = 0; index < mainchain.bonds.size(); index++)\r
- {\r
- tmpBond = (Bond) mainchain.bonds.elementAt(index);\r
- if (tmpBond.at1.alignmentMapping == ii - 1)\r
- {\r
- if (highlightBond1 != null)\r
- {\r
- highlightBond1.at2.isSelected = false;\r
- }\r
-\r
- if (highlightBond2 != null)\r
- {\r
- highlightBond2.at1.isSelected = false;\r
- }\r
-\r
- highlightBond1 = null;\r
- highlightBond2 = null;\r
-\r
- if (index > 0)\r
- {\r
- highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
- highlightBond1.at2.isSelected = true;\r
- }\r
-\r
- if (index != mainchain.bonds.size())\r
- {\r
- highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
- highlightBond2.at1.isSelected = true;\r
- }\r
-\r
- break;\r
- }\r
- }\r
-\r
- redrawneeded = true;\r
- repaint();\r
- }\r
-\r
- public void setAllchainsVisible(boolean b)\r
- {\r
- for (int ii = 0; ii < pdb.chains.size(); ii++)\r
- {\r
- PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);\r
- chain.isVisible = b;\r
- }\r
- mainchain.isVisible = true;\r
- findCentre();\r
- setupBonds();\r
- }\r
-\r
-\r
- //////////////////////////////////\r
- ///StructureListener\r
- public String getPdbFile()\r
- {\r
- return "???";\r
- }\r
-\r
-\r
- String lastMessage;\r
- public void mouseOverStructure(int pdbResNum, String chain)\r
- {\r
- if (lastMessage == null || !lastMessage.equals(pdbResNum+chain))\r
- ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());\r
-\r
- lastMessage = pdbResNum+chain;\r
- }\r
-\r
- StringBuffer resetLastRes = new StringBuffer();\r
- StringBuffer eval = new StringBuffer();\r
-\r
- public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)\r
- {\r
- if (!seqColoursReady)\r
- {\r
- return;\r
- }\r
-\r
- if (highlightRes != null\r
- && highlightRes.contains( (atomIndex - 1) + ""))\r
- {\r
- return;\r
- }\r
-\r
- int index = -1;\r
- Bond tmpBond;\r
- for (index = 0; index < mainchain.bonds.size(); index++)\r
- {\r
- tmpBond = (Bond) mainchain.bonds.elementAt(index);\r
- if (tmpBond.at1.atomIndex == atomIndex)\r
- {\r
- if (highlightBond1 != null)\r
- {\r
- highlightBond1.at2.isSelected = false;\r
- }\r
-\r
- if (highlightBond2 != null)\r
- {\r
- highlightBond2.at1.isSelected = false;\r
- }\r
-\r
- highlightBond1 = null;\r
- highlightBond2 = null;\r
-\r
- if (index > 0)\r
- {\r
- highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
- highlightBond1.at2.isSelected = true;\r
- }\r
-\r
- if (index != mainchain.bonds.size())\r
- {\r
- highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
- highlightBond2.at1.isSelected = true;\r
- }\r
-\r
- break;\r
- }\r
- }\r
-\r
- redrawneeded = true;\r
- repaint();\r
- }\r
-\r
- public void updateColours(Object source)\r
- {\r
- AlignmentPanel ap = (AlignmentPanel) source;\r
- colourBySequence(ap.getSequenceRenderer(),\r
- ap.av.getShowSequenceFeatures() ?\r
- ap.getFeatureRenderer() : null);\r
- redrawneeded = true;\r
- repaint();\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package MCview;
+
+import java.io.*;
+import java.util.*;
+
+// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+
+import jalview.appletgui.*;
+import jalview.structure.*;
+
+public class AppletPDBCanvas
+ extends Panel implements MouseListener, MouseMotionListener, StructureListener
+{
+
+ MCMatrix idmat = new MCMatrix(3, 3);
+ MCMatrix objmat = new MCMatrix(3, 3);
+ boolean redrawneeded = true;
+ int omx = 0;
+ int mx = 0;
+ int omy = 0;
+ int my = 0;
+ public PDBfile pdb;
+ PDBEntry pdbentry;
+ int bsize;
+ Image img;
+ Graphics ig;
+ Dimension prefsize;
+ float[] centre = new float[3];
+ float[] width = new float[3];
+ float maxwidth;
+ float scale;
+ String inStr;
+ String inType;
+ boolean bysequence = true;
+ boolean depthcue = true;
+ boolean wire = false;
+ boolean bymolecule = false;
+ boolean zbuffer = true;
+ boolean dragging;
+ int xstart;
+ int xend;
+ int ystart;
+ int yend;
+ int xmid;
+ int ymid;
+ Font font = new Font("Helvetica", Font.PLAIN, 10);
+ public SequenceI [] sequence;
+ final StringBuffer mappingDetails = new StringBuffer();
+ String appletToolTip = null;
+ int toolx, tooly;
+ PDBChain mainchain;
+ Vector highlightRes;
+ boolean pdbAction = false;
+ Bond highlightBond1, highlightBond2;
+ boolean errorLoading = false;
+ boolean seqColoursReady = false;
+ FeatureRenderer fr;
+ AlignmentPanel ap;
+ StructureSelectionManager ssm;
+
+ public AppletPDBCanvas(PDBEntry pdbentry,
+ SequenceI[] seq,
+ AlignmentPanel ap,
+ String protocol)
+
+ {
+ this.ap = ap;
+ this.pdbentry = pdbentry;
+ this.sequence = seq;
+
+ ssm = StructureSelectionManager.getStructureSelectionManager();
+
+ try{
+ pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
+ if (fr!=null)
+ fr.featuresAdded();
+ }catch(Exception ex)
+ {
+ ex.printStackTrace();
+ return;
+ }
+
+ pdbentry.setId(pdb.id);
+
+ ssm.addStructureViewerListener(this);
+
+ colourBySequence(ap.getSequenceRenderer(),
+ ap.av.getShowSequenceFeatures() ?
+ ap.getFeatureRenderer() : null);
+
+ int max = -10;
+ int maxchain = -1;
+ int pdbstart = 0;
+ int pdbend = 0;
+ int seqstart = 0;
+ int seqend = 0;
+ AlignSeq maxAlignseq = null;
+
+ //JUST DEAL WITH ONE SEQUENCE FOR NOW
+ SequenceI sequence = seq[0];
+
+ for (int i = 0; i < pdb.chains.size(); i++)
+ {
+
+ mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +
+ ( (PDBChain) pdb.chains.elementAt(i)).sequence.
+ getSequenceAsString());
+ mappingDetails.append("\nNo of residues = " +
+ ( (PDBChain) pdb.chains.elementAt(i)).residues.size() +
+ "\n\n");
+
+ // Now lets compare the sequences to get
+ // the start and end points.
+ // Align the sequence to the pdb
+ AlignSeq as = new AlignSeq(sequence,
+ ( (PDBChain) pdb.chains.elementAt(i)).sequence,
+ "pep");
+ as.calcScoreMatrix();
+ as.traceAlignment();
+ PrintStream ps = new PrintStream(System.out)
+ {
+ public void print(String x)
+ {
+ mappingDetails.append(x);
+ }
+
+ public void println()
+ {
+ mappingDetails.append("\n");
+ }
+ };
+
+ as.printAlignment(ps);
+
+ if (as.maxscore > max)
+ {
+ max = as.maxscore;
+ maxchain = i;
+
+ pdbstart = as.seq2start;
+ pdbend = as.seq2end;
+ seqstart = as.seq1start + sequence.getStart() - 1;
+ seqend = as.seq1end + sequence.getEnd() - 1;
+ maxAlignseq = as;
+ }
+
+ mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
+ mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
+ }
+
+ mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
+
+ mainchain.pdbstart = pdbstart;
+ mainchain.pdbend = pdbend;
+ mainchain.seqstart = seqstart;
+ mainchain.seqend = seqend;
+ mainchain.isVisible = true;
+ // mainchain.makeExactMapping(maxAlignseq, sequence);
+ // mainchain.transferRESNUMFeatures(sequence, null);
+ this.pdb = pdb;
+ this.prefsize = new Dimension(getSize().width, getSize().height);
+
+ //Initialize the matrices to identity
+ for (int i = 0; i < 3; i++)
+ {
+ for (int j = 0; j < 3; j++)
+ {
+ if (i != j)
+ {
+ idmat.addElement(i, j, 0);
+ objmat.addElement(i, j, 0);
+ }
+ else
+ {
+ idmat.addElement(i, j, 1);
+ objmat.addElement(i, j, 1);
+ }
+ }
+ }
+
+ addMouseMotionListener(this);
+ addMouseListener(this);
+
+ addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ doKeyPressed(evt);
+ }
+ });
+
+ findCentre();
+ findWidth();
+
+ setupBonds();
+
+ scale = findScale();
+ }
+
+ Vector visiblebonds;
+ void setupBonds()
+ {
+ seqColoursReady = false;
+ // Sort the bonds by z coord
+ visiblebonds = new Vector();
+
+ for (int ii = 0; ii < pdb.chains.size(); ii++)
+ {
+ if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ {
+ Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+
+ for (int i = 0; i < tmp.size(); i++)
+ {
+ visiblebonds.addElement(tmp.elementAt(i));
+ }
+ }
+ }
+ seqColoursReady = true;
+ colourBySequence(ap.getSequenceRenderer(),
+ ap.av.getShowSequenceFeatures() ?
+ ap.getFeatureRenderer() : null);
+ redrawneeded = true;
+ repaint();
+ }
+
+ public void findWidth()
+ {
+ float[] max = new float[3];
+ float[] min = new float[3];
+
+ max[0] = (float) - 1e30;
+ max[1] = (float) - 1e30;
+ max[2] = (float) - 1e30;
+
+ min[0] = (float) 1e30;
+ min[1] = (float) 1e30;
+ min[2] = (float) 1e30;
+
+ for (int ii = 0; ii < pdb.chains.size(); ii++)
+ {
+ if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ {
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+
+ for (int i = 0; i < bonds.size(); i++)
+ {
+ Bond tmp = (Bond) bonds.elementAt(i);
+
+ if (tmp.start[0] >= max[0])
+ {
+ max[0] = tmp.start[0];
+ }
+
+ if (tmp.start[1] >= max[1])
+ {
+ max[1] = tmp.start[1];
+ }
+
+ if (tmp.start[2] >= max[2])
+ {
+ max[2] = tmp.start[2];
+ }
+
+ if (tmp.start[0] <= min[0])
+ {
+ min[0] = tmp.start[0];
+ }
+
+ if (tmp.start[1] <= min[1])
+ {
+ min[1] = tmp.start[1];
+ }
+
+ if (tmp.start[2] <= min[2])
+ {
+ min[2] = tmp.start[2];
+ }
+
+ if (tmp.end[0] >= max[0])
+ {
+ max[0] = tmp.end[0];
+ }
+
+ if (tmp.end[1] >= max[1])
+ {
+ max[1] = tmp.end[1];
+ }
+
+ if (tmp.end[2] >= max[2])
+ {
+ max[2] = tmp.end[2];
+ }
+
+ if (tmp.end[0] <= min[0])
+ {
+ min[0] = tmp.end[0];
+ }
+
+ if (tmp.end[1] <= min[1])
+ {
+ min[1] = tmp.end[1];
+ }
+
+ if (tmp.end[2] <= min[2])
+ {
+ min[2] = tmp.end[2];
+ }
+ }
+ }
+ }
+
+ width[0] = (float) Math.abs(max[0] - min[0]);
+ width[1] = (float) Math.abs(max[1] - min[1]);
+ width[2] = (float) Math.abs(max[2] - min[2]);
+
+ maxwidth = width[0];
+
+ if (width[1] > width[0])
+ {
+ maxwidth = width[1];
+ }
+
+ if (width[2] > width[1])
+ {
+ maxwidth = width[2];
+ }
+
+ // System.out.println("Maxwidth = " + maxwidth);
+ }
+
+ public float findScale()
+ {
+ int dim;
+ int width;
+ int height;
+
+ if (getSize().width != 0)
+ {
+ width = getSize().width;
+ height = getSize().height;
+ }
+ else
+ {
+ width = prefsize.width;
+ height = prefsize.height;
+ }
+
+ if (width < height)
+ {
+ dim = width;
+ }
+ else
+ {
+ dim = height;
+ }
+
+ return (float) (dim / (1.5d * maxwidth));
+ }
+
+ public void findCentre()
+ {
+ float xtot = 0;
+ float ytot = 0;
+ float ztot = 0;
+
+ int bsize = 0;
+
+ //Find centre coordinate
+ for (int ii = 0; ii < pdb.chains.size(); ii++)
+ {
+ if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+ {
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+
+ bsize += bonds.size();
+
+ for (int i = 0; i < bonds.size(); i++)
+ {
+ xtot = xtot + ( (Bond) bonds.elementAt(i)).start[0] +
+ ( (Bond) bonds.elementAt(i)).end[0];
+
+ ytot = ytot + ( (Bond) bonds.elementAt(i)).start[1] +
+ ( (Bond) bonds.elementAt(i)).end[1];
+
+ ztot = ztot + ( (Bond) bonds.elementAt(i)).start[2] +
+ ( (Bond) bonds.elementAt(i)).end[2];
+ }
+ }
+ }
+
+ centre[0] = xtot / (2 * (float) bsize);
+ centre[1] = ytot / (2 * (float) bsize);
+ centre[2] = ztot / (2 * (float) bsize);
+ }
+
+ public void paint(Graphics g)
+ {
+
+ if (errorLoading)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setColor(Color.black);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString("Error loading PDB data!!", 50, getSize().height / 2);
+ return;
+ }
+
+ if (!seqColoursReady)
+ {
+ g.setColor(Color.black);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString("Fetching PDB data...", 50, getSize().height / 2);
+ return;
+ }
+
+ //Only create the image at the beginning -
+ //this saves much memory usage
+ if ( (img == null) || (prefsize.width != getSize().width) ||
+ (prefsize.height != getSize().height))
+ {
+
+ try
+ {
+ prefsize.width = getSize().width;
+ prefsize.height = getSize().height;
+
+ scale = findScale();
+ img = createImage(prefsize.width, prefsize.height);
+ ig = img.getGraphics();
+
+ redrawneeded = true;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ if (redrawneeded)
+ {
+ drawAll(ig, prefsize.width, prefsize.height);
+ redrawneeded = false;
+ }
+ if (appletToolTip != null)
+ {
+ ig.setColor(Color.red);
+ ig.drawString(appletToolTip, toolx, tooly);
+ }
+
+ g.drawImage(img, 0, 0, this);
+
+ pdbAction = false;
+ }
+
+ public void drawAll(Graphics g, int width, int height)
+ {
+ ig.setColor(Color.black);
+ ig.fillRect(0, 0, width, height);
+ drawScene(ig);
+ drawLabels(ig);
+ }
+
+ public void setColours(jalview.schemes.ColourSchemeI cs)
+ {
+ bysequence = false;
+ pdb.setColours(cs);
+ redrawneeded = true;
+ repaint();
+ }
+
+
+
+ // This method has been taken out of PDBChain to allow
+ // Applet and Application specific sequence renderers to be used
+ void colourBySequence(SequenceRenderer sr, FeatureRenderer fr)
+ {
+ StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
+
+ boolean showFeatures = false;
+ if (fr!=null)
+ {
+ if (fr == null)
+ {
+ fr = new jalview.appletgui.FeatureRenderer(ap.av);
+ }
+ fr.transferSettings(fr);
+ showFeatures = true;
+ }
+
+ PDBChain chain;
+ if (bysequence && pdb != null)
+ {
+ for (int ii = 0; ii < pdb.chains.size(); ii++)
+ {
+ chain = (PDBChain) pdb.chains.elementAt(ii);
+
+ for (int i = 0; i < chain.bonds.size(); i++)
+ {
+ Bond tmp = (Bond) chain.bonds.elementAt(i);
+ tmp.startCol = Color.lightGray;
+ tmp.endCol = Color.lightGray;
+ if (chain != mainchain)
+ {
+ continue;
+ }
+
+ for (int s = 0; s < sequence.length; s++)
+ {
+ for (int m = 0; m < mapping.length; m++)
+ {
+ if (mapping[m].getSequence() == sequence[s])
+ {
+ int pos = mapping[m].getSeqPos(tmp.at1.resNumber)-1;
+ if (pos > 0)
+ {
+ pos = sequence[s].findIndex(pos);
+ tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
+ if (showFeatures)
+ {
+ tmp.startCol = fr.findFeatureColour(tmp.startCol,
+ sequence[s],
+ pos);
+ }
+ }
+ pos = mapping[m].getSeqPos(tmp.at2.resNumber)-1;
+ if (pos > 0)
+ {
+ pos = sequence[s].findIndex(pos);
+ tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
+ if (showFeatures)
+ {
+ tmp.endCol = fr.findFeatureColour(tmp.endCol,
+ sequence[s],
+ pos);
+ }
+ }
+
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ Zsort zsort;
+ public void drawScene(Graphics g)
+ {
+ if (zbuffer)
+ {
+ if (zsort == null)
+ {
+ zsort = new Zsort();
+ }
+
+ zsort.Zsort(visiblebonds);
+ }
+
+ Bond tmpBond = null;
+ for (int i = 0; i < visiblebonds.size(); i++)
+ {
+ tmpBond = (Bond) visiblebonds.elementAt(i);
+
+ xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
+ (getSize().width / 2));
+ ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
+ (getSize().height / 2));
+
+ xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
+ (getSize().width / 2));
+ yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
+ (getSize().height / 2));
+
+ xmid = (xend + xstart) / 2;
+ ymid = (yend + ystart) / 2;
+
+ if (depthcue && !bymolecule)
+ {
+ if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
+ {
+ g.setColor(tmpBond.startCol.darker().darker());
+ drawLine(g, xstart, ystart, xmid, ymid);
+
+ g.setColor(tmpBond.endCol.darker().darker());
+ drawLine(g, xmid, ymid, xend, yend);
+ }
+ else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
+ {
+ g.setColor(tmpBond.startCol.darker());
+ drawLine(g, xstart, ystart, xmid, ymid);
+
+ g.setColor(tmpBond.endCol.darker());
+ drawLine(g, xmid, ymid, xend, yend);
+ }
+ else
+ {
+ g.setColor(tmpBond.startCol);
+ drawLine(g, xstart, ystart, xmid, ymid);
+
+ g.setColor(tmpBond.endCol);
+ drawLine(g, xmid, ymid, xend, yend);
+ }
+
+ }
+ else if (depthcue && bymolecule)
+ {
+ if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
+ {
+ g.setColor(Color.green.darker().darker());
+ drawLine(g, xstart, ystart, xend, yend);
+ }
+ else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
+ {
+ g.setColor(Color.green.darker());
+ drawLine(g, xstart, ystart, xend, yend);
+ }
+ else
+ {
+ g.setColor(Color.green);
+ drawLine(g, xstart, ystart, xend, yend);
+ }
+ }
+ else if (!depthcue && !bymolecule)
+ {
+ g.setColor(tmpBond.startCol);
+ drawLine(g, xstart, ystart, xmid, ymid);
+ g.setColor(tmpBond.endCol);
+ drawLine(g, xmid, ymid, xend, yend);
+ }
+ else
+ {
+ drawLine(g, xstart, ystart, xend, yend);
+ }
+
+ if (highlightBond1 != null && highlightBond1 == tmpBond)
+ {
+ g.setColor(Color.white);
+ drawLine(g, xmid, ymid, xend, yend);
+ }
+
+ if (highlightBond2 != null && highlightBond2 == tmpBond)
+ {
+ g.setColor(Color.white);
+ drawLine(g, xstart, ystart, xmid, ymid);
+ }
+
+ }
+ }
+
+ public void drawLine(Graphics g, int x1, int y1, int x2, int y2)
+ {
+ if (!wire)
+ {
+ if ( ( (float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
+ {
+ g.drawLine(x1, y1, x2, y2);
+ g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
+ g.drawLine(x1, y1 - 1, x2, y2 - 1);
+ }
+ else
+ {
+ g.setColor(g.getColor().brighter());
+ g.drawLine(x1, y1, x2, y2);
+ g.drawLine(x1 + 1, y1, x2 + 1, y2);
+ g.drawLine(x1 - 1, y1, x2 - 1, y2);
+ }
+ }
+ else
+ {
+ g.drawLine(x1, y1, x2, y2);
+ }
+ }
+
+ public Dimension minimumsize()
+ {
+ return prefsize;
+ }
+
+ public Dimension preferredsize()
+ {
+ return prefsize;
+ }
+
+ public void doKeyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_UP)
+ {
+ scale = (float) (scale * 1.1);
+ redrawneeded = true;
+ repaint();
+ }
+ else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+ {
+ scale = (float) (scale * 0.9);
+ redrawneeded = true;
+ repaint();
+ }
+ }
+
+ public void mousePressed(MouseEvent e)
+ {
+ pdbAction = true;
+ Atom fatom = findAtom(e.getX(), e.getY());
+ if (fatom != null)
+ {
+ fatom.isSelected = !fatom.isSelected;
+
+ redrawneeded = true;
+ repaint();
+ if (foundchain != -1)
+ {
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ if (chain == mainchain)
+ {
+ if (fatom.alignmentMapping != -1)
+ {
+ if (highlightRes == null)
+ {
+ highlightRes = new Vector();
+ }
+
+ if (highlightRes.contains(fatom.alignmentMapping + "" + ""))
+ {
+ highlightRes.removeElement(fatom.alignmentMapping + "");
+ }
+ else
+ {
+ highlightRes.addElement(fatom.alignmentMapping + "");
+ }
+ }
+ }
+ }
+
+ }
+ mx = e.getX();
+ my = e.getY();
+ omx = mx;
+ omy = my;
+ dragging = false;
+ }
+
+ public void mouseMoved(MouseEvent e)
+ {
+ pdbAction = true;
+ if (highlightBond1 != null)
+ {
+ highlightBond1.at2.isSelected = false;
+ highlightBond2.at1.isSelected = false;
+ highlightBond1 = null;
+ highlightBond2 = null;
+ }
+
+ Atom fatom = findAtom(e.getX(), e.getY());
+
+ PDBChain chain = null;
+ if (foundchain != -1)
+ {
+ chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ if (chain == mainchain)
+ {
+ mouseOverStructure(fatom.resNumber, chain.id);
+ }
+ }
+
+ if (fatom != null)
+ {
+ toolx = e.getX();
+ tooly = e.getY();
+
+ appletToolTip = chain.id + ":" + fatom.resNumber + " " + fatom.resName;
+ redrawneeded = true;
+ repaint();
+ }
+ else
+ {
+ mouseOverStructure(-1, chain!=null?chain.id:null);
+ appletToolTip = null;
+ redrawneeded = true;
+ repaint();
+ }
+ }
+
+ public void mouseClicked(MouseEvent e)
+ {
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ }
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ int x = evt.getX();
+ int y = evt.getY();
+ mx = x;
+ my = y;
+
+ MCMatrix objmat = new MCMatrix(3, 3);
+ objmat.setIdentity();
+
+ if ( (evt.getModifiers() & Event.META_MASK) != 0)
+ {
+ objmat.rotatez( (float) ( (mx - omx)));
+ }
+ else
+ {
+ objmat.rotatex( (float) ( (my - omy)));
+ objmat.rotatey( (float) ( (omx - mx)));
+ }
+
+ //Alter the bonds
+ for (int ii = 0; ii < pdb.chains.size(); ii++)
+ {
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+
+ for (int i = 0; i < bonds.size(); i++)
+ {
+ Bond tmpBond = (Bond) bonds.elementAt(i);
+
+ //Translate the bond so the centre is 0,0,0
+ tmpBond.translate( -centre[0], -centre[1], -centre[2]);
+
+ //Now apply the rotation matrix
+ tmpBond.start = objmat.vectorMultiply(tmpBond.start);
+ tmpBond.end = objmat.vectorMultiply(tmpBond.end);
+
+ //Now translate back again
+ tmpBond.translate(centre[0], centre[1], centre[2]);
+ }
+ }
+
+ objmat = null;
+
+ omx = mx;
+ omy = my;
+
+ dragging = true;
+
+ redrawneeded = true;
+
+ repaint();
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ dragging = false;
+ return;
+ }
+
+ void drawLabels(Graphics g)
+ {
+
+ for (int ii = 0; ii < pdb.chains.size(); ii++)
+ {
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+
+ if (chain.isVisible)
+ {
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+
+ for (int i = 0; i < bonds.size(); i++)
+ {
+ Bond tmpBond = (Bond) bonds.elementAt(i);
+
+ if (tmpBond.at1.isSelected)
+ {
+ labelAtom(g, tmpBond, 1);
+ }
+
+ if (tmpBond.at2.isSelected)
+ {
+
+ labelAtom(g, tmpBond, 2);
+ }
+ }
+ }
+ }
+ }
+
+ public void labelAtom(Graphics g, Bond b, int n)
+ {
+ g.setFont(font);
+
+ if (n == 1)
+ {
+ int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +
+ (getSize().width / 2));
+ int ystart = (int) ( ( (b.start[1] - centre[1]) * scale) +
+ (getSize().height / 2));
+
+ g.setColor(Color.red);
+ g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
+ }
+
+ if (n == 2)
+ {
+ int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +
+ (getSize().width / 2));
+ int ystart = (int) ( ( (b.end[1] - centre[1]) * scale) +
+ (getSize().height / 2));
+
+ g.setColor(Color.red);
+ g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
+ }
+ }
+
+ int foundchain = -1;
+ public Atom findAtom(int x, int y)
+ {
+ Atom fatom = null;
+
+ foundchain = -1;
+
+ for (int ii = 0; ii < pdb.chains.size(); ii++)
+ {
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ int truex;
+ Bond tmpBond = null;
+
+ if (chain.isVisible)
+ {
+ Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+
+ for (int i = 0; i < bonds.size(); i++)
+ {
+ tmpBond = (Bond) bonds.elementAt(i);
+
+ truex = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
+ (getSize().width / 2));
+
+ if (Math.abs(truex - x) <= 2)
+ {
+ int truey = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
+ (getSize().height / 2));
+
+ if (Math.abs(truey - y) <= 2)
+ {
+ fatom = tmpBond.at1;
+ foundchain = ii;
+ break;
+ }
+ }
+ }
+
+ // Still here? Maybe its the last bond
+
+ truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
+ (getSize().width / 2));
+
+ if (Math.abs(truex - x) <= 2)
+ {
+ int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
+ (getSize().height / 2));
+
+ if (Math.abs(truey - y) <= 2)
+ {
+ fatom = tmpBond.at2;
+ foundchain = ii;
+ break;
+ }
+ }
+
+ }
+
+ if (fatom != null) //)&& chain.ds != null)
+ {
+ chain = (PDBChain) pdb.chains.elementAt(foundchain);
+ }
+ }
+
+ return fatom;
+ }
+
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ public void highlightRes(int ii)
+ {
+ if (!seqColoursReady)
+ {
+ return;
+ }
+
+ if (highlightRes != null
+ && highlightRes.contains( (ii - 1) + ""))
+ {
+ return;
+ }
+
+ int index = -1;
+ Bond tmpBond;
+ for (index = 0; index < mainchain.bonds.size(); index++)
+ {
+ tmpBond = (Bond) mainchain.bonds.elementAt(index);
+ if (tmpBond.at1.alignmentMapping == ii - 1)
+ {
+ if (highlightBond1 != null)
+ {
+ highlightBond1.at2.isSelected = false;
+ }
+
+ if (highlightBond2 != null)
+ {
+ highlightBond2.at1.isSelected = false;
+ }
+
+ highlightBond1 = null;
+ highlightBond2 = null;
+
+ if (index > 0)
+ {
+ highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+ highlightBond1.at2.isSelected = true;
+ }
+
+ if (index != mainchain.bonds.size())
+ {
+ highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+ highlightBond2.at1.isSelected = true;
+ }
+
+ break;
+ }
+ }
+
+ redrawneeded = true;
+ repaint();
+ }
+
+ public void setAllchainsVisible(boolean b)
+ {
+ for (int ii = 0; ii < pdb.chains.size(); ii++)
+ {
+ PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+ chain.isVisible = b;
+ }
+ mainchain.isVisible = true;
+ findCentre();
+ setupBonds();
+ }
+
+
+ //////////////////////////////////
+ ///StructureListener
+ public String getPdbFile()
+ {
+ return "???";
+ }
+
+
+ String lastMessage;
+ public void mouseOverStructure(int pdbResNum, String chain)
+ {
+ if (lastMessage == null || !lastMessage.equals(pdbResNum+chain))
+ ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
+
+ lastMessage = pdbResNum+chain;
+ }
+
+ StringBuffer resetLastRes = new StringBuffer();
+ StringBuffer eval = new StringBuffer();
+
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ {
+ if (!seqColoursReady)
+ {
+ return;
+ }
+
+ if (highlightRes != null
+ && highlightRes.contains( (atomIndex - 1) + ""))
+ {
+ return;
+ }
+
+ int index = -1;
+ Bond tmpBond;
+ for (index = 0; index < mainchain.bonds.size(); index++)
+ {
+ tmpBond = (Bond) mainchain.bonds.elementAt(index);
+ if (tmpBond.at1.atomIndex == atomIndex)
+ {
+ if (highlightBond1 != null)
+ {
+ highlightBond1.at2.isSelected = false;
+ }
+
+ if (highlightBond2 != null)
+ {
+ highlightBond2.at1.isSelected = false;
+ }
+
+ highlightBond1 = null;
+ highlightBond2 = null;
+
+ if (index > 0)
+ {
+ highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+ highlightBond1.at2.isSelected = true;
+ }
+
+ if (index != mainchain.bonds.size())
+ {
+ highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+ highlightBond2.at1.isSelected = true;
+ }
+
+ break;
+ }
+ }
+
+ redrawneeded = true;
+ repaint();
+ }
+
+ public void updateColours(Object source)
+ {
+ AlignmentPanel ap = (AlignmentPanel) source;
+ colourBySequence(ap.getSequenceRenderer(),
+ ap.av.getShowSequenceFeatures() ?
+ ap.getFeatureRenderer() : null);
+ redrawneeded = true;
+ repaint();
+ }
+
+
+}
git://source.jalview.org / jalview.git / commitdiff